Tuesday, 13 November 2012

We developed software for detecting somatic mutations in cancer based on exome sequencing data, Genomon, implemented on the supercomputer system of Human Genome Center at the University of Tokyo. We will introduce details of Genomon and discuss its future.

Phosphorylation of the histone variant y-H2AX forms H2AX that marks DNA double-strand breaks. Our findings based on the whole-genome landscape of H2AX and y-H2AX in resting and proliferating cells before and after ionizing irradiation provide insight into DNA repair programs in cancer and may have implications for cancer therapy.

Several pathologically different lung cancer subtypes are analyzed by next-generation sequencing to find somatic variations. The results demonstrate that this approach is useful to detect previously known recurrent mutations as well as novel variations.

ChIP and Methyl Sequencing, Dissecting the Subtleties of the GenomeMasoud Toloue, VP of Genomic Research, Bioo Scientific Corporation, United States of America

Strategies for massive parallel sequencing have
revolutionized research across diverse scientific disciplines. Despite these advances methylated DNA immunoprecipitation, methyl-binding domain, and
restriction enzyme based reduced methyl sequencing all need micrograms of genomic DNA, making them incompatible with laser capture microdissection or
rare stem cell populations. We will present our latest ChIP and Methyl-Seq data on genome wide comparisons between differentiated and un-differentiated tissues and explain the significance of these patterns.

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. We report the sequencing and assembly of the oyster genome using short-reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response, and proteome of shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. Expansion of heat shock protein 70 and of inhibitors of apoptosis is likely central to the oyster’s adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

Next-generation sequencing technologies are now inspiring a new understanding of the bacterial transcriptome. In this talk, it will be highlighted how this new emerging technology is now revolutionizing our understanding of the complexity, plasticity and regulation of bacterial transcriptomes.

The combination of RNA Seq and RNA biochemistry is enabling a deeper understanding of the post-transcriptional regulation of gene expression. Until recently the efficiency of next-generation sequencing has limited the number and depth of RNA Seq studies. Ion Torrent Semiconductor Sequencing™ delivers RNA sequencing at an unprecedented speed, scalability and cost enabling in depth analysis of post-transcriptional gene regulation.

17:00

Drinks Reception

Wednesday, 14 November 2012

The MIQE guidelines address the urgent need for improvements to qPCR assay design, implementation and data analysis. Their widespread acceptance, demonstrated by over 700 citations in the peer-reviewed literature, has made them a universal tool for measuring qPCR assay quality.

10:15

Technology Spotlight:Application of Automated Molecular Diagnostic System for Infectious Diesases Based on Real Time PCRDoo-Sung Cheon, Deputy Scientific Director , Korea Centers for Disease Control and Prevention

Automatic molecular diagnostic system integrated with HTS genome extraction module and real time PCR is presented for illustrating practical diagnostic application of taqman based real time PCR on several infecious diseases targets including enteric viruses, bioterrorism and viral hepatitis.

A versatile approach is presented for multiple mutations detection based on multicolor melting analysis, which features high throughput, no post-PCR manipulations and wide compatibility with existing real-time PCR platforms.

qPCR Based Diagnostics & Applications

11:45

Keynote Presentation

The Use of -omic Technologies for Biomarker DevelopmentMichael Pfaffl, Professor, Technical University of Munich, Germany

Biomarkers have been used extensively across diagnostic and therapeutic areas over many life science disciplines. Herein we developed and validate “transcribed biomarkers” for the detection of hormone abuse, to guarantee wholesome food.

12:15

Technology Spotlight:The New LightCycler® 96 System: it is so Easy to be a Lab HeroRalf Mauritz, Director, Roche Applied Science

The new LightCycler® 96 system is a benchtop instrument that can handle up to 96 samples using standard 96 multi well plates or 8-tube strips. A new optical module is developed that is based on 2x 96 glass fibres with 4 excitation and 4 emission filters. A white LED is used as light source and a CCD camera as detection unit. This setup supports the most common PCR formats used in the market like SYBR Green I and Hydrolysis Probes and thus enables the user to perform all common PCR applications.

Expression profiling of individual cells collected from tissue is exceeding powerful to reveal the biologically complexity. It is here used to characterize astrocyte development in the brain and also during healing after brain injury.

Direct PCR of Isolated Single Cells on a Microfluidic Device for the Genomic Quantification Izumi Kubo, Professor, Soka University, Japan

An original microfluidic device for the high-throughput isolation of single cells and its application to novel PCR/RT-PCR technique for genomic quantification of the isolated cells is described in this presentation.